The Synthetic Biology Software Suite

Main

The Synthetic Biology Software Suite (SynBioSS) is a software suite for the generation, storing, retrieval and quantitative simulation of synthetic biological networks. SynBioSS facilitates computational synthetic biology and consists of three independent components: the Desktop Simulator (DS), the Wiki, and the Designer.

Downloadable Desktop Simulator

The SynBioSS DS is a set of multiscale algorithms for modeling and simulating reaction networks, such as gene regulatory networks. It combines routines for modeling systems stochastically and discretely (kinetic Monte Carlo) and/or stochastically and continuously (stochastic differential equations). SynBioSS has a user friendly graphical user interface, and it reads and writes SBML and .nc models. SynBioSS DS can run on Windows, Mac OS, and Linux/UNIX. It is an Open Source software and can be downloaded at SourceForge. Click here to download SynBioSS DS.

Designer

SynBioSS Designer is a web service to transform a sequence of BioBricks, or any other set of biomolecular components, to a set of reactions that can be simulated dynamically in SynBioSS DS. The user simply inputs the Biobricks and their relationships and Designer builds a reaction network using biological interactions rules. Click here to go to the Designer.

SynBioSS Wiki

SynBioSS Wiki is a web service to collect the kinetic parameters necessary to create a model that can be simulated by SynBioSS DS. If you want to create a model in from the SynBioSS Wiki reaction by reaction, click here to go to the SynBioSS Wiki. Also, if you want to add or edit any information on biochemical species and / or the reactions in which they participate, go to the Wiki.

SynBioSS Desktop Simulator Examples(DS)

If you are not quite sure how to get started making a model, or just want to see what SynBioSS DS can do, here are some example models that can be loaded into SynBioSS DS.